'''
imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/l5c1_350_.tif'
#imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/L1CH2_maxp_300-374sampleframe.tif'
imp = IJ.openImage(imgpath)
#ntd = NucToDots(imp)
#ntd.stackCLAHE(imp)
#imp.show()
#ppimp =ntd.preprocess(imp)
#ppimp.show()
#maximp = NucToDots(imp).run()
#maximp.show()
ntd = NucToDots(imp);
ntd.run()
for i in ntd.getXcoordA():
print i
IJ.log('test ')
dlh = DLH(imp, 2, 15) # linkrange, distance
# becareful with the swapped X and Y axis
#dlh.setData(jarray.array(ntd.getXcoords(), 'i'), jarray.array(ntd.getYcoords(), 'i'), jarray.array(ntd.getFrame(), 'i'))
dlh.setData(ntd.getXcoordA(), ntd.getYcoordA(), ntd.getFrameA())
nearestneighbor = LinkCostsOnlyDistance()
dlh.doLinking(nearestneighbor, False)
# convert to Tracks object
tracks = VecTrajectoryToTracks().runsimple(dlh.getAll_traj())
tracks.accept(TrackReLinker())
from emblcmci.linker.costfunctions import LinkCostsOnlyDistance from emblcmci.linker import ViewDynamics as VD from de.embl.cmci.obj.converters import VecTrajectoryToTracks from de.embl.cmci.seg import NucleusExtractor import jarray ''' a test code for preprocessing nucleus image to derive maxima and then get track ''' imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/l5c1_350_CLAHE.tif' #imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/L1CH2_maxp_300-374sampleframe.tif' #imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/l5c1_CLAHE.tif' imp = IJ.openImage(imgpath) ntd = NucToDots(imp); #ntd.run() imp2 = ntd.preprocessCoreStack(imp) # for imp that is already stackCLAHEed. #for i in ntd.getXcoordA(): # print i imp2.show() print "Extracting Nucleus ..." #subwwhh = 110 # this must be guessed in the pre-run, by doing particle analysis and get the approximate sizes. en = NucleusExtractor(imp) #en.constructNodesByPA(imp2) ns = en.getPerNucleusBinImgProcessors(imp, imp2) # for i in range(10): # ImagePlus(str(i), ns.get(i).getBinip()).show()
and then get track ... mdofied for extracting positive class images and negative class images. ''' imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/l5c1_350_CLAHE.tif' #imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/L1CH2_maxp_300-374sampleframe.tif' #imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/l5c1_CLAHE.tif' #imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/l5c1_fastCLAHE.tif' #imgpath = '/Volumes/D/Julia20130201-/almfscreen/samples_112712/l1/CH2_maxp.tif' #imgpath = '/Volumes/D/Julia20130201-/almfscreen/samples_112712/l2/l2c1.tif' #imgpath = '/Volumes/D/Julia20130201-/almfscreen/samples_112712/l3/l3c1.tif' #imgpath = '/Volumes/D/Julia20130201-/almfscreen/samples_112712/l4/l4c1.tif' imgpath = '/Volumes/D/Julia20130201-/almfscreen/samples_112712/l5/l5c1.tif' imp = IJ.openImage(imgpath) ntd = NucToDots(imp); ntd.run() # runs CLAHE first, takes a bit of time. #ntd.runmain() # for imp that is already stackCLAHEed. #for i in ntd.getXcoordA(): # print i print "Extracting Nucleus ..." subwwhh = 130 # this must be guessed in the pre-run, by doing particle analysis and get the approximate sizes. WATERSHED_THRESHOLD = 0.10; en = NucleusExtractor(imp, ntd.getXcoordA(), ntd.getYcoordA(), ntd.getFrameA()) en.constructNodesByDots(subwwhh, WATERSHED_THRESHOLD) print 'node length before filtering: ' + str(en.getNodes().size()) en.analyzeDotsandBinImages() print 'node length after filtering: ' + str(en.getNodes().size())
''' imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/l5c1_350_.tif' #imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/L1CH2_maxp_300-374sampleframe.tif' imp = IJ.openImage(imgpath) #ntd = NucToDots(imp) #ntd.stackCLAHE(imp) #imp.show() #ppimp =ntd.preprocess(imp) #ppimp.show() #maximp = NucToDots(imp).run() #maximp.show() ntd = NucToDots(imp); ntd.run() subwwhh = 120 # size of sub image # from here is the extraction ''' nrp = NRP() nrp.getPerNucleusBinImgProcessors(imp, subwwhh, ntd.getXcoordA(), ntd.getYcoordA(), ntd.getFrameA()) stk = nrp.getBinStack(); ''' en = NucleusExtractor(imp, ntd.getXcoordA(), ntd.getYcoordA(), ntd.getFrameA()) en.constructNodes(subwwhh) en.analyzeDotsandBinImages() nodes = en.getNodes() stk = ImageStack(subwwhh, subwwhh)
